Predicting β-lactam susceptibility from the genome of Streptococcus pneumoniae and other mitis group streptococci

Frontiers in Microbiology

Microbiology

Patricia Shewmaker¹  Kurt Fuursted²  Hans-Christian Slotved²  Helle Brander Eriksen³  Christian Salgård Jensen⁴  Kristian Schønning⁴  Anders Jensen⁵  Ana Rita Rebelo⁶  Frank Møller Aarestrup⁶  Jens Jørgen Christensen⁷  Xiaohui Nielsen⁷ 

[1] Centers for Disease Control and Prevention, Atlanta, GA, United States;Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark;Department of Clinical Microbiology, Herlev and Gentofte Hospital, Herlev, Denmark;Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark;Department of Clinical Microbiology, Sygehus Lillebælt, Vejle, Denmark;Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark;The Regional Department of Clinical Microbiology, Slagelse, Denmark;Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark;

关键词: penicillin-binding proteins;    penicillin;    genotypic susceptibility;    pneumococcus;    Streptococcus;   

DOI  :  10.3389/fmicb.2023.1120023

 received in 2022-12-09, accepted in 2023-02-13,  发布年份 2023

来源: Frontiers

【 摘 要 】

IntroductionFor Streptococcus pneumoniae, β-lactam susceptibility can be predicted from the amino acid sequence of the penicillin-binding proteins PBP1a, PBP2b, and PBP2x. The combination of PBP-subtypes provides a PBP-profile, which correlates to a phenotypic minimal inhibitory concentration (MIC). The non-S. pneumoniae Mitis-group streptococci (MGS) have similar PBPs and exchange pbp-alleles with S. pneumoniae. We studied whether a simple BLAST analysis could be used to predict phenotypic susceptibility in Danish S. pneumoniae isolates and in internationally collected MGS.MethodIsolates with available WGS and phenotypic susceptibility data were included. For each isolate, the best matching PBP-profile was identified by BLAST analysis. The corresponding MICs for penicillin and ceftriaxone was retrieved. Category agreement (CA), minor-, major-, and very major discrepancy was calculated. Genotypic-phenotypic accuracy was examined with Deming regression.ResultsAmong 88 S. pneumoniae isolates, 55 isolates had a recognized PBP-profile, and CA was 100% for penicillin and 98.2% for ceftriaxone. In 33 S. pneumoniae isolates with a new PBP-profile, CA was 90.9% (penicillin) and 93.8% (ceftriaxone) using the nearest recognized PBP-profile. Applying the S. pneumoniae database to non-S. pneumoniae MGS revealed that none had a recognized PBP-profile. For Streptococcus pseudopneumoniae, CA was 100% for penicillin and ceftriaxone in 19 susceptible isolates. In 33 Streptococcus mitis isolates, CA was 75.8% (penicillin) and 86.2% (ceftriaxone) and in 25 Streptococcus oralis isolates CA was 8% (penicillin) and 100% (ceftriaxone).ConclusionUsing a simple BLAST analysis, genotypic susceptibility prediction was accurate in Danish S. pneumoniae isolates, particularly in isolates with recognized PBP-profiles. Susceptibility was poorly predicted in other MGS using the current database.

【 授权许可】

Unknown   
Copyright © 2023 Eriksen, Fuursted, Jensen, Jensen, Nielsen, Christensen, Shewmaker, Rebelo, Aarestrup, Schønning, Slotved and the One Day in Denmark (ODiD) Consortium.